Re: [Pytables-users] Speed of CArray writing sparse matrices

2013-06-24 Thread Anthony Scopatz
Hello Giovanni, Great to hear that everything is working much better for you now and that everything is much faster and smaller than NPY ;) Do you know how the default value is set btw? This is computed via a magical heuristic algorithm written by Francesc (?) called computechunksize(). This i

Re: [Pytables-users] Speed of CArray writing sparse matrices

2013-06-24 Thread Giovanni Luca Ciampaglia
Hi Anthony, thanks for the explanation and the links, it's much clearer now. So without compression a CArray is really a smarter type of sparse file, but you have to set a sensible chunk shape. Do you know how the default value is set btw? I am asking because I didn't see any change in performa

Re: [Pytables-users] Speed of CArray writing sparse matrices

2013-06-22 Thread Anthony Scopatz
Hi Giovanni! I think that you may have some misunderstanding about how chucking works, which is leading you to get terrible performance. In fact what you describe is a great strategy (right all and zip) for using normal Arrays. However, chunking and CArrays don't work like this. If a chunk cont

[Pytables-users] Speed of CArray writing sparse matrices

2013-06-22 Thread Giovanni Luca Ciampaglia
Hi all, I have a sparse 3.4M x 3.4M adjacency matrix with nnz = 23M and wanted to see if CArray was an appropriate solution for storing it. Right now I am using the NumPy binary format for storing the data in coordinate format and loading the matrix with Scipy's sparse coo_matrix class. As far